PYRF - HALSA - GREMLIN Contacts

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PYRF - Orotidine 5'-phosphate decarboxylase

UniProt:	Q9P9M3	Sequences: MSFVEELGARIEAADSVVSVGLDPDMERLPEDVQDAELPRWAFNRRIIDATHEHAAVFKPNAAFYEDSDGWRALRETVAYAHGKGVPVLLDAKRADIGNTARQYAEILAHVDAITVNPYLGEDALQPFLTQDEAGVFVLCRTSNEGGMDFQHLELAAYDRRLYEHVAERAAEWNAQYGDVGLVVGATAPDELQAIRERVPELPFLVPGVGAQGGDAEAAVEYGLNDDGVGLVNSTRGVIFAGEHGSAWAAAAGDAARTLRERLNRHR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	267 (253)
Sequences:	1664 (1013)
Seq/√Len:	63.7

HALSA - PYRF

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
234_S	237_G	4.646	1.00
41_W	76_E	4.429	1.00
160_R	168_E	3.721	1.00
255_A	258_T	3.278	1.00
44_N	77_T	3.152	1.00
54_H	253_G	3.146	1.00
92_A	114_I	2.989	1.00
78_V	88_V	2.974	1.00
44_N	65_Y	2.892	1.00
90_L	108_L	2.861	1.00
49_D	80_Y	2.829	1.00
53_E	253_G	2.763	1.00
170_A	182_L	2.613	1.00
215_D	218_A	2.610	1.00
90_L	111_V	2.339	1.00
139_L	142_T	2.291	1.00
62_A	90_L	2.281	1.00
126_Q	130_T	2.276	1.00
42_A	46_R	2.260	1.00
101_A	128_F	2.256	1.00
45_R	80_Y	2.251	1.00
65_Y	77_T	2.193	1.00
161_R	164_E	2.192	1.00
102_R	130_T	2.160	1.00
170_A	180_V	2.112	1.00
56_A	231_L	2.103	1.00
57_V	89_L	2.069	1.00
47_I	51_T	2.062	1.00
114_I	136_V	1.997	1.00
137_F	181_G	1.887	1.00
62_A	108_L	1.833	1.00
150_F	169_R	1.807	1.00
110_H	134_A	1.787	1.00
174_N	178_G	1.745	0.99
75_R	79_A	1.709	0.99
10_R	13_A	1.708	0.99
160_R	165_H	1.683	0.99
51_T	58_F	1.680	0.99
168_E	198_R	1.662	0.99
140_C	182_L	1.650	0.99
141_R	147_G	1.619	0.99
167_A	182_L	1.612	0.99
58_F	81_A	1.594	0.99
68_S	72_R	1.579	0.99
68_S	75_R	1.579	0.99
20_V	238_V	1.578	0.99
169_R	172_E	1.566	0.99
9_A	13_A	1.564	0.99
164_E	194_A	1.563	0.99
62_A	92_A	1.557	0.99
81_A	86_V	1.554	0.99
74_L	90_L	1.549	0.99
141_R	152_H	1.541	0.99
251_A	254_D	1.521	0.99
119_Y	166_V	1.512	0.99
22_L	44_N	1.497	0.98
118_P	166_V	1.478	0.98
150_F	162_L	1.472	0.98
116_V	136_V	1.457	0.98
78_V	111_V	1.454	0.98
257_R	261_E	1.451	0.98
40_R	73_A	1.442	0.98
48_I	77_T	1.413	0.98
66_E	94_R	1.409	0.98
116_V	128_F	1.400	0.98
67_D	70_G	1.388	0.97
242_G	247_A	1.378	0.97
140_C	167_A	1.361	0.97
129_L	136_V	1.353	0.97
46_R	248_W	1.352	0.97
136_V	180_V	1.352	0.97
124_A	146_G	1.322	0.97
69_D	72_R	1.318	0.96
15_D	53_E	1.303	0.96
116_V	138_V	1.284	0.96
58_F	86_V	1.281	0.96
242_G	245_G	1.278	0.96
241_A	252_A	1.266	0.96
41_W	45_R	1.263	0.95
126_Q	173_W	1.258	0.95
138_V	170_A	1.254	0.95
62_A	71_W	1.241	0.95
55_A	86_V	1.240	0.95
90_L	114_I	1.231	0.95
154_E	161_R	1.227	0.95
45_R	77_T	1.223	0.95
71_W	108_L	1.212	0.94
253_G	257_R	1.210	0.94
234_S	255_A	1.207	0.94
46_R	249_A	1.192	0.94
51_T	81_A	1.184	0.94
122_E	166_V	1.180	0.94
251_A	255_A	1.178	0.93
30_P	35_D	1.169	0.93
25_D	99_N	1.167	0.93
25_D	28_R	1.157	0.93
19_S	57_V	1.140	0.92
154_E	159_D	1.133	0.92
53_E	86_V	1.133	0.92
234_S	238_V	1.129	0.92
15_D	86_V	1.119	0.92
164_E	168_E	1.104	0.91
78_V	82_H	1.103	0.91
195_I	199_V	1.095	0.91
209_V	234_S	1.090	0.90
206_V	214_G	1.088	0.90
190_D	194_A	1.073	0.90
174_N	179_D	1.068	0.90
66_E	107_I	1.061	0.89
47_I	239_I	1.060	0.89
60_P	74_L	1.051	0.89
37_E	73_A	1.046	0.89
92_A	108_L	1.042	0.88
11_I	231_L	1.041	0.88
88_V	111_V	1.037	0.88
209_V	216_A	1.029	0.88
141_R	191_E	1.021	0.87
44_N	73_A	1.013	0.87
38_L	41_W	1.010	0.87
36_A	42_A	1.004	0.86
82_H	88_V	0.995	0.86
237_G	259_L	0.994	0.86
252_A	256_A	0.994	0.86
122_E	173_W	0.991	0.86
120_L	124_A	0.987	0.85
165_H	169_R	0.984	0.85
20_V	55_A	0.978	0.85
10_R	55_A	0.970	0.84
74_L	111_V	0.969	0.84
81_A	214_G	0.964	0.84
254_D	257_R	0.959	0.84
141_R	188_A	0.957	0.84
71_W	90_L	0.956	0.84
209_V	232_V	0.952	0.83
20_V	51_T	0.947	0.83
158_Y	161_R	0.944	0.83
68_S	71_W	0.942	0.83
258_T	262_R	0.942	0.83
17_V	220_V	0.941	0.83
129_L	173_W	0.933	0.82
250_A	254_D	0.932	0.82
148_M	188_A	0.928	0.82
123_D	126_Q	0.922	0.81
146_G	149_D	0.920	0.81
62_A	74_L	0.916	0.81
122_E	129_L	0.915	0.81
117_N	124_A	0.912	0.81
57_V	231_L	0.911	0.81
138_V	180_V	0.910	0.80
38_L	42_A	0.909	0.80
182_L	204_F	0.904	0.80
51_T	252_A	0.902	0.80
182_L	199_V	0.901	0.80
34_Q	39_P	0.896	0.79
37_E	40_R	0.891	0.79
54_H	257_R	0.885	0.79
48_I	81_A	0.883	0.78
28_R	239_I	0.882	0.78
123_D	173_W	0.875	0.78
147_G	174_N	0.875	0.78
194_A	197_E	0.872	0.78
155_L	158_Y	0.871	0.77
28_R	240_F	0.867	0.77
52_H	86_V	0.865	0.77
145_E	148_M	0.850	0.76
41_W	80_Y	0.848	0.76
200_P	204_F	0.846	0.75
141_R	189_P	0.844	0.75
36_A	39_P	0.843	0.75
9_A	12_E	0.832	0.74
20_V	47_I	0.832	0.74
215_D	219_A	0.831	0.74
88_V	113_A	0.830	0.74
245_G	252_A	0.828	0.74
155_L	165_H	0.823	0.73
8_G	227_D	0.821	0.73
72_R	75_R	0.820	0.73
125_L	138_V	0.819	0.73
148_M	152_H	0.815	0.73
112_D	134_A	0.812	0.72
196_R	199_V	0.812	0.72
140_C	170_A	0.811	0.72
207_P	210_G	0.809	0.72
74_L	108_L	0.807	0.72
191_E	194_A	0.805	0.72
206_V	230_G	0.805	0.72
89_L	233_N	0.802	0.71
189_P	222_Y	0.800	0.71
254_D	258_T	0.800	0.71
212_Q	236_R	0.798	0.71
117_N	139_L	0.794	0.71
214_G	218_A	0.787	0.70
64_F	99_N	0.786	0.70
234_S	259_L	0.783	0.70
22_L	65_Y	0.774	0.69
152_H	188_A	0.767	0.68
137_F	203_P	0.761	0.67
20_V	233_N	0.760	0.67
155_L	159_D	0.757	0.67
77_T	80_Y	0.754	0.67
217_E	262_R	0.752	0.66
122_E	170_A	0.751	0.66
224_L	229_V	0.750	0.66
167_A	204_F	0.750	0.66
81_A	88_V	0.749	0.66
164_E	198_R	0.744	0.66
183_V	207_P	0.744	0.66
129_L	180_V	0.742	0.65
150_F	166_V	0.741	0.65
108_L	141_R	0.740	0.65
214_G	222_Y	0.738	0.65
10_R	85_G	0.729	0.64
256_A	260_R	0.723	0.63
108_L	114_I	0.723	0.63
247_A	250_A	0.722	0.63
154_E	158_Y	0.721	0.63
78_V	110_H	0.718	0.63
227_D	230_G	0.718	0.63
116_V	129_L	0.717	0.63
218_A	221_E	0.716	0.63
109_A	128_F	0.716	0.63
152_H	191_E	0.714	0.62
158_Y	165_H	0.713	0.62
138_V	171_A	0.713	0.62
92_A	95_A	0.711	0.62
153_L	162_L	0.707	0.62
122_E	149_D	0.706	0.62
22_L	77_T	0.706	0.62
53_E	257_R	0.703	0.61
51_T	86_V	0.698	0.61
182_L	200_P	0.695	0.60
174_N	202_L	0.692	0.60
147_G	189_P	0.689	0.60
125_L	146_G	0.683	0.59
67_D	107_I	0.681	0.59
114_I	118_P	0.681	0.59
24_P	65_Y	0.680	0.59
35_D	106_E	0.679	0.59
87_P	135_G	0.678	0.58
38_L	76_E	0.676	0.58
95_A	124_A	0.671	0.58
101_A	116_V	0.667	0.57
199_V	202_L	0.667	0.57
165_H	168_E	0.666	0.57
8_G	12_E	0.665	0.57
248_W	252_A	0.665	0.57
155_L	160_R	0.664	0.57
149_D	169_R	0.663	0.57
60_P	98_G	0.660	0.56
153_L	165_H	0.658	0.56
170_A	173_W	0.658	0.56
82_H	110_H	0.653	0.56
119_Y	163_Y	0.651	0.55
193_Q	221_E	0.650	0.55
9_A	72_R	0.649	0.55
24_P	240_F	0.647	0.55
224_L	230_G	0.646	0.55
7_L	11_I	0.646	0.55
51_T	109_A	0.643	0.55
99_N	102_R	0.643	0.55
99_N	120_L	0.642	0.54
253_G	256_A	0.641	0.54
104_Y	183_V	0.641	0.54
27_E	34_Q	0.637	0.54
210_G	236_R	0.635	0.54
192_L	222_Y	0.634	0.53
139_L	166_V	0.634	0.53
52_H	84_K	0.633	0.53
167_A	191_E	0.632	0.53
196_R	230_G	0.632	0.53
171_A	201_E	0.632	0.53
207_P	236_R	0.631	0.53
62_A	114_I	0.631	0.53
7_L	57_V	0.630	0.53
208_G	236_R	0.629	0.53
31_E	34_Q	0.628	0.53
45_R	49_D	0.628	0.53
63_A	94_R	0.626	0.53
147_G	151_Q	0.625	0.52
6_E	112_D	0.623	0.52
47_I	167_A	0.622	0.52
207_P	212_Q	0.620	0.52
94_R	104_Y	0.619	0.52
104_Y	235_T	0.615	0.51
92_A	107_I	0.613	0.51
216_A	255_A	0.613	0.51
50_A	249_A	0.611	0.51
61_N	99_N	0.611	0.51
50_A	250_A	0.609	0.51
77_T	81_A	0.609	0.51
188_A	191_E	0.608	0.50
64_F	107_I	0.604	0.50
133_E	179_D	0.604	0.50
69_D	75_R	0.604	0.50
48_I	51_T	0.604	0.50
182_L	202_L	0.602	0.50
147_G	219_A	0.602	0.50
190_D	193_Q	0.602	0.50
32_D	246_S	0.602	0.50
18_V	256_A	0.600	0.50
66_E	70_G	0.599	0.49
63_A	104_Y	0.597	0.49
250_A	253_G	0.596	0.49
245_G	248_W	0.594	0.49
158_Y	175_A	0.594	0.49
92_A	111_V	0.592	0.49
18_V	259_L	0.587	0.48
28_R	43_F	0.586	0.48
167_A	170_A	0.586	0.48
167_A	199_V	0.585	0.48
255_A	259_L	0.584	0.48
183_V	210_G	0.583	0.48
26_M	35_D	0.582	0.47
76_E	80_Y	0.581	0.47
74_L	192_L	0.581	0.47
48_I	84_K	0.580	0.47
105_A	127_P	0.580	0.47
158_Y	217_E	0.579	0.47
152_H	189_P	0.579	0.47
54_H	256_A	0.579	0.47
161_R	194_A	0.578	0.47
143_S	187_T	0.578	0.47
207_P	213_G	0.578	0.47
66_E	181_G	0.577	0.47
24_P	60_P	0.576	0.47
6_E	10_R	0.574	0.47
122_E	126_Q	0.572	0.46
258_T	261_E	0.572	0.46
26_M	40_R	0.571	0.46
74_L	92_A	0.569	0.46
61_N	64_F	0.564	0.45
64_F	240_F	0.562	0.45
61_N	135_G	0.562	0.45
167_A	195_I	0.558	0.45
47_I	81_A	0.557	0.45
79_A	197_E	0.556	0.44
238_V	241_A	0.554	0.44
226_D	246_S	0.552	0.44
124_A	149_D	0.549	0.44
120_L	233_N	0.548	0.44
48_I	80_Y	0.548	0.44
237_G	255_A	0.545	0.43
113_A	133_E	0.542	0.43
133_E	245_G	0.541	0.43
40_R	44_N	0.540	0.43
29_L	35_D	0.537	0.42
67_D	103_Q	0.535	0.42
7_L	203_P	0.534	0.42
87_P	90_L	0.534	0.42
123_D	169_R	0.533	0.42
13_A	85_G	0.533	0.42
37_E	72_R	0.533	0.42
11_I	141_R	0.532	0.42
80_Y	83_G	0.532	0.42
93_K	96_D	0.532	0.42
206_V	233_N	0.531	0.42
57_V	232_V	0.530	0.42
27_E	72_R	0.530	0.42
31_E	35_D	0.528	0.41
79_A	257_R	0.527	0.41
26_M	30_P	0.525	0.41
214_G	234_S	0.523	0.41
233_N	237_G	0.522	0.41
259_L	262_R	0.518	0.40
79_A	133_E	0.517	0.40
193_Q	197_E	0.516	0.40
41_W	77_T	0.515	0.40
187_T	212_Q	0.515	0.40
28_R	64_F	0.515	0.40
214_G	241_A	0.513	0.40
51_T	55_A	0.512	0.40
94_R	183_V	0.511	0.39
237_G	240_F	0.508	0.39
150_F	153_L	0.507	0.39
155_L	161_R	0.506	0.39
139_L	170_A	0.504	0.39
63_A	66_E	0.503	0.39
24_P	28_R	0.501	0.38
62_A	88_V	0.500	0.38
224_L	228_G	0.500	0.38

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3n3mA	2	0.9775	100	0.361	Contact Map
2ffcA	2	0.9738	100	0.368	Contact Map
3r89A	2	0.985	100	0.371	Contact Map
4mjzA	2	0.9738	100	0.373	Contact Map
3v75A	2	0.9738	100	0.376	Contact Map
2fdsA	2	0.9625	100	0.376	Contact Map
3qw4B	4	0.9438	100	0.414	Contact Map
3qw3A	2	0.9176	100	0.436	Contact Map
3gdmA	2	0.8464	100	0.586	Contact Map
3ewwA	2	0.8352	100	0.691	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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